#!/usr/bin/env python # Copyright (c) 2007 NHLBI, NIH # Copyright (c) 2007 The George Washington University # Authors: Chongzhi Zang, Weiqun Peng, Dustin E Schones and Keji Zhao # # This software is distributable under the terms of the GNU General # Public License (GPL) v2, the text of which can be found at # http://www.gnu.org/copyleft/gpl.html. Installing, importing or # otherwise using this module constitutes acceptance of the terms of # this License. # # Disclaimer # # This software is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # Comments and/or additions are welcome (send e-mail to: # schonesde@mail.nih.gov) """ This module contains classes of genome data, e.g. chromsomes per species, the size of the chromosomes, etc. """ import re, os, sys, shutil GenomeDataError = "Error in GenomeData class"; bg_number_chroms = 1; bg_length_of_chrom = 100000000; background_chroms = []; background_chrom_lengths = {}; for i in range(0,bg_number_chroms): background_chroms.append( 'chr' + str(i+1)); background_chrom_lengths['chr' + str(i+1)] = bg_length_of_chrom; mm8_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', 'chr18','chr19','chrX', 'chrY', 'chrM'] mm9_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', 'chr18','chr19','chrX', 'chrY', 'chrM'] rn4_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', 'chr18','chr19','chr20','chrX','chrM'] hg18_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', 'chr18','chr19','chr20','chr21','chr22','chrX','chrY','chrM'] hg19_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17', 'chr18','chr19','chr20','chr21','chr22','chrX','chrY','chrM'] sacCer1_chroms = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9', 'chr10','chr11','chr12','chr13','chr14','chr15','chr16','chrM'] dm2_chroms = ['chr2h', 'chr2L', 'chr2R', 'chr3h', 'chr3L', 'chr3R','chr4','chr4h','chrM','chrU','chrX','chrXh','chrYh'] dm3_chroms = ['chr2L', 'chr2LHet', 'chr2R', 'chr2RHet', 'chr3L', 'chr3LHet', 'chr3R', 'chr3RHet', 'chr4','chrX','chrXHet', 'chrYHet', 'chrU', 'chrUextra', 'chrM'] pombe_chroms = ['chr1','chr2', 'chr3', 'mat']; mm8_chrom_lengths = {'chr1':197069962, 'chr2':181976762, 'chr3':159872112, 'chr4':155029701, 'chr5':152003063, 'chr6':149525685, 'chr7':145134094, 'chr8':132085098, 'chr9':124000669, 'chr10':129959148, 'chr11':121798632, 'chr12':120463159, 'chr13':120614378, 'chr14':123978870, 'chr15':103492577, 'chr16':98252459, 'chr17':95177420, 'chr18':90736837, 'chr19':61321190, 'chrX':165556469, 'chrY':16029404, 'chrM':16299} mm9_chrom_lengths = {'chr1':197195432, 'chr2':181748087, 'chr3':159599783, 'chr4':155630120, 'chr5':152537259, 'chr6':149517037, 'chr7':152524553, 'chr8':131738871, 'chr9':124076172, 'chr10':129993255, 'chr11':121843856, 'chr12':121257530, 'chr13':120284312, 'chr14':125194864, 'chr15':103494974, 'chr16':98319150, 'chr17':95272651, 'chr18':90772031, 'chr19':61342430, 'chrX':166650296, 'chrY':15902555, 'chrM':16299} rn4_chrom_lengths = {'chr1':267910886, 'chr2':258207540, 'chr3':171063335, 'chr4':187126005, 'chr5':173096209, 'chr6':147636619, 'chr7':143002779, 'chr8':129041809, 'chr9':113440463, 'chr10':110718848, 'chr11':87759784, 'chr12':46782294, 'chr13':111154910, 'chr14':112194335, 'chr15':109758846, 'chr16':90238779, 'chr17':97296363, 'chr18':87265094, 'chr19':59218465, 'chr20':55268282, 'chrX':160699376, 'chrM':16300} hg18_chrom_lengths = {'chr1':247249719, 'chr2':242951149, 'chr3':199501827, 'chr4':191273063, 'chr5':180857866, 'chr6':170899992, 'chr7':158821424, 'chr8':146274826, 'chr9':140273252, 'chr10':135374737, 'chr11':134452384, 'chr12':132349534, 'chr13':114142980, 'chr14':106368585, 'chr15':100338915, 'chr16':88827254, 'chr17':78774742, 'chr18':76117153, 'chr19':63811651, 'chr20':62435964, 'chr21':46944323, 'chr22':49691432, 'chrX':154913754, 'chrY':57772954, 'chrM':16571} hg19_chrom_lengths = {'chr1':249250621, 'chr2':243199373, 'chr3':198022430, 'chr4':191154276, 'chr5':180915260, 'chr6':171115067, 'chr7':159138663, 'chr8':146364022, 'chr9':141213431, 'chr10':135534747, 'chr11':135006516, 'chr12':133851895, 'chr13':115169878, 'chr14':107349540, 'chr15':102531392, 'chr16':90354753, 'chr17':81195210, 'chr18':78077248, 'chr19':59128983, 'chr20':63025520, 'chr21':48129895, 'chr22':51304566, 'chrX':155270560, 'chrY':59373566, 'chrM':16571} dm2_chrom_lengths = {'chr2h':1694122, 'chr2L':22407834, 'chr2R':20766785, 'chr3h':2955737, 'chr3L':23771897, 'chr3R':27905053, 'chr4h':88110, 'chr4':1281640, 'chrXh':359526, 'chrX':22224390, 'chrYh':396896, 'chrM':19517, 'chrU':8724946} dm3_chrom_lengths = {'chr2L':23011544, 'chr2LHet':368872, 'chr2R':21146708, 'chr2RHet':3288761, 'chr3L':24543557, 'chr3LHet':2555491, 'chr3R':27905053, 'chr3RHet':2517507, 'chr4':1351857, 'chrX':22422827, 'chrXHet':204112, 'chrYHet':347038, 'chrU':10049037, 'chrUextra':29004656, 'chrM':19517} sacCer1_chrom_lengths = {'chr1':230208, 'chr2':813136, 'chr3':316613, 'chr4':1531914, 'chr5':576869, 'chr6':270148, 'chr7':1090944, 'chr8':562639, 'chr9':439885, 'chr10':745446, 'chr11':666445, 'chr12':1078173, 'chr13':924430, 'chr14':784328, 'chr15':1091285, 'chr16':948060, 'chrM':85779} pombe_chrom_lengths = {'chr1':5580032,'chr2':4541604,'chr3':2453783, 'mat':41249} species_chroms = {'mm8':mm8_chroms, 'mm9':mm9_chroms, 'hg18':hg18_chroms, 'hg19':hg19_chroms, "dm2":dm2_chroms, "dm3":dm3_chroms, "sacCer1":sacCer1_chroms, "pombe":pombe_chroms, 'rn4':rn4_chroms, 'background':background_chroms}; species_chrom_lengths={'mm8':mm8_chrom_lengths, 'mm9':mm9_chrom_lengths, 'hg18':hg18_chrom_lengths, 'hg19':hg19_chrom_lengths, 'dm2':dm2_chrom_lengths, 'dm3':dm3_chrom_lengths, 'sacCer1':sacCer1_chrom_lengths, 'pombe':pombe_chrom_lengths, 'rn4':rn4_chrom_lengths, 'background':background_chrom_lengths};